Computation with biomolecules provides a basis for manufacturing high-density nano-scale computers. The massive parallel processing potential of such computers makes them ideally suited to solving small-scale NP-complete problems. Further, biomolecular-based computers allow for the embedded control of synthetic control systems and nano-fabrication techniques. Components suitable for use in biomolecular computers are generally compatible with biological environments. Accordingly, biomolecular computers can be used as logic controllers in biological systems generally unsuitable for incorporation of standard silicon-based chips.